October 04, 2014 @ Sen Lab - U of Michigan

Overview

Baseline Stationary Covariates

  • Binary : Sex, Cohort, Ethnicity, Age, Marital, Child,
  • Categorical(>2) : InstitutionID, Specialty
  • Continuous : EFE0, Neu0
  • 84 subjects

Methylation Data

  • Number of unique Genes : 23,369
  • Number of total CpG Sites : 481,178
  • Number of selected Genes : 27
  • Number of selected CpG Sites : 871

Goal

Baseline Stationary Covariates

  • Visualization (contingency tables, distribution plots)
  • Test for independence between Baseline covariates

Methylation Data

  • Gene Selection
  • Visualization of raw data (correlation, distribution)
  • Evaluate transformation methods

Test Results


Table: Fisher's Exact Test p-values

---------------------  ------
Sex by Age              0.016
Sex by Child            0.472
Sex by Cohort           1.000
Sex by Ethnicity        0.577
Sex by Marital          0.825
Age by Child            0.000
Age by Cohort           0.101
Age by Ethnicity        0.561
Age by Marital          0.351
Child by Cohort         1.000
Child by Ethnicity      0.193
Child by Marital        0.000
Cohort by Ethnicity     0.009
Cohort by Marital       0.613
Ethnicity by Marital    0.014
---------------------  ------

Table: Fisher's Exact Test p-values

---------------------------  ------
Sex by InstitutionID          0.975
Sex by Specialty              0.070
Age by InstitutionID          0.429
Age by Specialty              0.773
Child by InstitutionID        0.337
Child by Specialty            0.337
Cohort by InstitutionID       0.000
Cohort by Specialty           0.155
Ethnicity by InstitutionID    0.606
Ethnicity by Specialty        0.516
Marital by InstitutionID      0.257
Marital by Specialty          0.017
---------------------------  ------

Nonparametric test of EFE0 by Baseline Covariates


Table: Wilcoxon Test p-values

----------  -------
Sex          0.6283
Cohort       0.7173
Ethnicity    0.1309
Age          0.4145
Marital      0.4524
Child        0.7173
----------  -------

Table: Kruskal-Wallis Test p-values

--------------  -------
InstitutionID    0.2314
Specialty        0.1637
--------------  -------

Nonparametric Test of Neu0 by Baseline Covariates


Table: Wilcoxon Test p-values

----------  -------
Sex          0.1087
Cohort       0.1612
Ethnicity    0.9689
Age          0.3115
Marital      0.2351
Child        0.2713
----------  -------

Table: Kruskal-Wallis Test p-values

--------------  -------
InstitutionID    0.5788
Specialty        0.6468
--------------  -------

Contingency Tables

Sex by Age
Older Younger
Female 5 27
Male 21 30
Sex by Child
No Yes
Female 30 2
Male 45 7
Sex by Cohort
2011 2012
Female 8 24
Male 13 39
Sex by Ethnicity
Caucasian Other
Female 27 5
Male 40 12

Sex by Marital
NotSingle Single
Female 15 17
Male 23 29
Age by Child
No Yes
Older 18 8
Younger 56 1
Age by Cohort
2011 2012
Older 10 16
Younger 11 46
Age by Ethnicity
Caucasian Other
Older 20 6
Younger 47 10

Age by Marital
NotSingle Single
Older 14 12
Younger 24 33
Child by Cohort
2011 2012
No 19 56
Yes 2 7
Child by Ethnicity
Caucasian Other
No 58 17
Yes 9 0
Child by Marital
NotSingle Single
No 29 46
Yes 9 0

Cohort by Ethnicity
Caucasian Other
2011 12 9
2012 55 8
Cohort by Marital
NotSingle Single
2011 8 13
2012 30 33
Ethnicity by Marital
NotSingle Single
Caucasian 35 32
Other 3 14

Sex by InstitutionID
Harvard IUPUI MGH MUSC UofCinci UofIowa UofM Yale
Female 3 2 1 3 6 4 13 0
Male 5 2 2 8 9 6 18 2
Sex by Specialty
Emergency Medicine Family Practice Internal Medicine Med Peds Ob Gyn Other Pediatrics Psychiatry Surgery Transitional
Female 2 4 8 1 1 5 5 2 1 3
Male 1 1 13 1 0 18 4 1 8 4
Age by InstitutionID
Harvard IUPUI MGH MUSC UofCinci UofIowa UofM Yale
Older 3 0 1 3 3 4 10 2
Younger 5 4 2 7 12 6 21 0

Age by Specialty
Emergency Medicine Family Practice Internal Medicine Med Peds Ob Gyn Other Pediatrics Psychiatry Surgery Transitional
Older 1 2 9 0 0 5 2 0 4 3
Younger 2 3 12 2 1 17 7 3 5 4
Child by InstitutionID
Harvard IUPUI MGH MUSC UofCinci UofIowa UofM Yale
No 6 4 3 8 15 9 28 2
Yes 2 0 0 3 0 1 3 0
Child by Specialty
Emergency Medicine Family Practice Internal Medicine Med Peds Ob Gyn Other Pediatrics Psychiatry Surgery Transitional
No 3 3 19 2 1 22 7 3 7 7
Yes 0 2 2 0 0 1 2 0 2 0

Cohort by InstitutionID
Harvard IUPUI MGH MUSC UofCinci UofIowa UofM Yale
2011 5 0 0 1 0 0 13 2
2012 3 4 3 10 15 10 18 0
Cohort by Specialty
Emergency Medicine Family Practice Internal Medicine Med Peds Ob Gyn Other Pediatrics Psychiatry Surgery Transitional
2011 1 1 6 0 0 3 1 0 3 5
2012 2 4 15 2 1 20 8 3 6 2
Ethnicity by InstitutionID
Harvard IUPUI MGH MUSC UofCinci UofIowa UofM Yale
Caucasian 5 4 2 9 13 9 24 1
Other 3 0 1 2 2 1 7 1

Ethnicity by Specialty
Emergency Medicine Family Practice Internal Medicine Med Peds Ob Gyn Other Pediatrics Psychiatry Surgery Transitional
Caucasian 2 5 15 2 1 18 9 3 7 4
Other 1 0 6 0 0 5 0 0 2 3
Marital by InstitutionID
Harvard IUPUI MGH MUSC UofCinci UofIowa UofM Yale
NotSingle 3 2 0 7 4 6 16 0
Single 5 2 3 4 11 4 15 2
Marital by Specialty
Emergency Medicine Family Practice Internal Medicine Med Peds Ob Gyn Other Pediatrics Psychiatry Surgery Transitional
NotSingle 0 4 5 1 0 11 8 2 4 2
Single 3 1 16 1 1 12 1 1 5 5

InstitutionID by Specialty
Emergency Medicine Family Practice Internal Medicine Med Peds Ob Gyn Other Pediatrics Psychiatry Surgery Transitional
Harvard 0 0 5 0 0 1 0 0 1 1
IUPUI 0 0 0 0 0 2 0 1 0 1
MGH 0 0 0 0 0 1 1 0 1 0
MUSC 0 2 2 0 0 3 1 1 2 0
UofCinci 0 0 8 0 0 6 0 1 0 0
UofIowa 0 0 3 0 0 3 4 0 0 0
UofM 3 3 3 2 1 7 3 0 3 5
Yale 0 0 0 0 0 0 0 0 2 0

Age (as continuous)

Age Density Plot

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   min     q1 median   mean     q3    max     sd      n 
  24.0   26.0   27.0   27.2   28.0   34.0    1.9   83.0

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Age Box-Plot

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Early Family Experience (EFE0)

EFE0 Density Plot

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   min     q1 median   mean     q3    max     sd      n 
  0.00   6.00  10.50  12.30  16.20  38.00   8.83  84.00

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EFE0 Box-Plot

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Emotional Experience (Neu0)

Neu0 Density Plot

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   min     q1 median   mean     q3    max     sd      n 
  2.00  13.00  18.00  19.40  24.50  44.40   9.29  84.00

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Neu0 Box-Plot

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Methylation Data

List of Selected Genes (to be updated)

Gene Chromosome Num.Sites
BDNF 3 68
STK32C 2 145
DOK6 10 23
UBE2D3 17 30
DEPDC7 3 12
NDEL1 9 19
ACP1 12 4
NR3C1 18 41
GABRA3 23 8
MAST4 18 70
GFAP 9 21
ALDH1L1 16 33
SOX9 9 20
Gene Chromosome Num.Sites
GLUL 1 28
GJA1 19 16
GJB6 5 30
GRIK2 19 45
BEGAIN 6 37
SLC6A4 9 16
MORC1 16 14
ZBTB20 16 70
MECP2 23 17
PTPRM 10 21
AGTPBP1 22 7
TBC1D8 12 33
SLC6A15 4 26
FGF2 17 17

Global Methylation Correlation Plots

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Global Methylation beta vs. logit2 Transformation (by subj)

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Global Methylation beta vs. logit2 Transformation (subj 2)

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Global Methylaiton beta vs. logit 2 Transformation (CpG)

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Global Methylaiton beta vs. logit 2 Transformation (CpG)

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qq plots (all subjects)

qq plots (all subjs, 871 sites)

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qq plots (Female)

qq plots (Female, 871 sites)

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qq plots (Male)

qq plots (Male, 871 sites)

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CpG site with smallest p value

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p3 <- ggplot(plotdat2, aes(x = mv1), na.rm = TRUE) + geom_density() +

scale_x_continuous(limits = c(1, 3.5))

p4 <- ggplot(plotdat2, aes(x = mv2), na.rm = TRUE) + geom_density() +

scale_x_continuous(limits = c(1, 3.5))

```